:orphan:  .. only available via index, not via toctree

.. title:: Package Recipe 'bioconductor-dnafusion'
.. highlight: bash

bioconductor-dnafusion
======================

.. conda:recipe:: bioconductor-dnafusion
   :replaces_section_title:
   :noindex:

   Identification of gene fusions using paired\-end sequencing

   :homepage: https://bioconductor.org/packages/3.18/bioc/html/DNAfusion.html
   :license: GPL-3
   :recipe: /`bioconductor-dnafusion <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dnafusion>`_/`meta.yaml <https://github.com/bioconda/bioconda-recipes/tree/master/recipes/bioconductor-dnafusion/meta.yaml>`_

   DNAfusion can identify gene fusions such as EML4\-ALK based on paired\-end sequencing results. This package was developed using position deduplicated BAM files generated with the AVENIO Oncology Analysis Software. These files are made using the AVENIO ctDNA surveillance kit and Illumina Nextseq 500 sequencing. This is a targeted hybridization NGS approach and includes ALK\-specific but not EML4\-specific probes.


.. conda:package:: bioconductor-dnafusion

   |downloads_bioconductor-dnafusion| |docker_bioconductor-dnafusion|

   :versions:
      
      

      ``1.4.0-0``,  ``1.2.0-0``,  ``1.0.0-0``

      

   
   :depends bioconductor-bamsignals: ``>=1.34.0,<1.35.0``
   :depends bioconductor-biocbaseutils: ``>=1.4.0,<1.5.0``
   :depends bioconductor-biocgenerics: ``>=0.48.0,<0.49.0``
   :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0``
   :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0``
   :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0``
   :depends bioconductor-iranges: ``>=2.36.0,<2.37.0``
   :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0``
   :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0``
   :depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene: ``>=3.18.0,<3.19.0``
   :depends r-base: ``>=4.3,<4.4.0a0``
   :requirements:

   .. rubric:: Installation

  You need a conda-compatible package manager
  (currently either `micromamba <https://mamba.readthedocs.io>`_, `mamba <https://mamba.readthedocs.io>`_, or `conda <https://docs.conda.io/projects/conda>`_)
  and the Bioconda channel already activated (see :ref:`set-up-channels`).

  While any of above package managers is fine, it is currently recommended to use either
  micromamba or mamba (see `here <https://mamba.readthedocs.io>`_ for installation instructions).
  We will show all commands using mamba below, but the arguments are the same for the two
  others.

  Given that you already have a conda environment in which you want to have this package, install with::

      mamba install bioconductor-dnafusion

   and update with::

      mamba update bioconductor-dnafusion

  To create a new environment, run::

      mamba create --name myenvname bioconductor-dnafusion

  with ``myenvname`` being a reasonable name for the environment
  (see e.g. the `mamba docs <https://mamba.readthedocs.io>`_ for details and further options).

  Alternatively, use the docker container::

      docker pull quay.io/biocontainers/bioconductor-dnafusion:<tag>

   (see `bioconductor-dnafusion/tags`_ for valid values for ``<tag>``)


.. |downloads_bioconductor-dnafusion| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-dnafusion.svg?style=flat
   :target: https://anaconda.org/bioconda/bioconductor-dnafusion
   :alt:   (downloads)
.. |docker_bioconductor-dnafusion| image:: https://quay.io/repository/biocontainers/bioconductor-dnafusion/status
   :target: https://quay.io/repository/biocontainers/bioconductor-dnafusion
.. _`bioconductor-dnafusion/tags`: https://quay.io/repository/biocontainers/bioconductor-dnafusion?tab=tags


.. raw:: html

    <script>
        var package = "bioconductor-dnafusion";
        var versions = ["1.4.0","1.2.0","1.0.0"];
    </script>






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    :file: ../../templates/package_dashboard.html

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